Variant report

Variant	rs2680346
Chromosome Location	chr15:73527770-73527771
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:73075824..73078601-chr15:73525839..73528039,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000159322	Chromatin interaction
ENSG00000260898	Chromatin interaction

Extended variants
information (count: 69 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:67)

rs_ID	r²[population]
rs11072404	0.84[ASW][hapmap];1.00[CEU][hapmap];0.94[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12592184	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs1320241	0.84[ASW][hapmap];1.00[CEU][hapmap];0.89[GIH][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1479336	1.00[CEU][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1620369	1.00[CEU][hapmap];0.89[GIH][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1621216	1.00[CEU][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1631796	1.00[CEU][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1678246	1.00[CEU][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1678247	1.00[CEU][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs16957640	1.00[CEU][hapmap]
rs1871387	1.00[CEU][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1979409	0.81[LWK][hapmap];0.92[YRI][hapmap]
rs2619257	1.00[CEU][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2619258	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2623989	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2623991	1.00[CEU][hapmap];0.89[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2623992	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2623995	0.87[AFR][1000 genomes]
rs2623999	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2660822	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2660825	1.00[CEU][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2660826	0.84[ASW][hapmap];0.80[LWK][hapmap];0.84[YRI][hapmap];0.84[AFR][1000 genomes]
rs2660828	1.00[CEU][hapmap];0.82[CHB][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2680333	0.85[AFR][1000 genomes]
rs2680336	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2680337	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2680342	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2680345	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs28619899	0.81[ASN][1000 genomes]
rs4564531	1.00[CEU][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4570800	1.00[CEU][hapmap];0.88[GIH][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs471192	1.00[CEU][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4776627	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4776629	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs481579	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs484515	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs484544	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs489873	0.92[ASW][hapmap];1.00[CEU][hapmap];0.94[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.81[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs494493	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs497539	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs499098	1.00[CEU][hapmap];0.89[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs513744	0.88[EUR][1000 genomes]
rs525587	1.00[CEU][hapmap];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs529004	1.00[ASW][hapmap];1.00[CEU][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.84[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs542259	1.00[CEU][hapmap];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs549377	0.83[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs553238	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs55787640	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs561929	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs58859253	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs59537860	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6495056	1.00[CEU][hapmap]
rs66881913	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs66931013	0.90[EUR][1000 genomes]
rs67999476	0.86[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs68053508	0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs68123262	0.90[EUR][1000 genomes]
rs7163504	1.00[CEU][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs7168651	0.90[EUR][1000 genomes]
rs7168829	0.90[EUR][1000 genomes]
rs7170328	1.00[CEU][hapmap]
rs7177629	0.85[CEU][hapmap]
rs8033192	1.00[CEU][hapmap]
rs8037761	1.00[CEU][hapmap];0.94[GIH][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8039308	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs8041219	1.00[CEU][hapmap]
rs9806271	1.00[CEU][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv525462	chr15:73349633-73563495	Genic enhancers Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
2	nsv904343	chr15:73396760-73775043	Strong transcription Bivalent Enhancer Enhancers Flanking Active TSS ZNF genes & repeats Weak transcription Genic enhancers Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:67 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:73493400-73528600	Weak transcription	Cortex derived primary cultured neurospheres	brain
2	chr15:73497800-73541800	Weak transcription	Fetal Kidney	kidney
3	chr15:73509600-73528800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr15:73516600-73528200	Weak transcription	Duodenum Mucosa	Duodenum
5	chr15:73516800-73528600	Weak transcription	Fetal Muscle Trunk	muscle
6	chr15:73517600-73528400	Weak transcription	Fetal Lung	lung
7	chr15:73518200-73528600	Weak transcription	Skeletal Muscle Male	skeletal muscle
8	chr15:73518200-73540800	Weak transcription	Colonic Mucosa	Colon
9	chr15:73518400-73531800	Weak transcription	Aorta	Aorta
10	chr15:73518600-73528600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr15:73518600-73528600	Weak transcription	Sigmoid Colon	Sigmoid Colon
12	chr15:73518600-73528800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
13	chr15:73518600-73529800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr15:73518600-73534000	Weak transcription	Right Ventricle	heart
15	chr15:73518800-73546200	Weak transcription	Psoas Muscle	Psoas
16	chr15:73518800-73547800	Weak transcription	Left Ventricle	heart
17	chr15:73520400-73528400	Weak transcription	Rectal Mucosa Donor 29	rectum
18	chr15:73520400-73528600	Weak transcription	Brain Anterior Caudate	brain
19	chr15:73520400-73528600	Weak transcription	Rectal Smooth Muscle	rectum
20	chr15:73520400-73562400	Weak transcription	H9 Cell Line	embryonic stem cell
21	chr15:73520600-73579600	Weak transcription	Colon Smooth Muscle	Colon
22	chr15:73520800-73536400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
23	chr15:73523000-73572200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
24	chr15:73523200-73547800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr15:73523800-73530200	Weak transcription	Adipose Nuclei	Adipose
26	chr15:73524200-73528600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
27	chr15:73524200-73529000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
28	chr15:73524200-73536600	Weak transcription	Skeletal Muscle Female	skeletal muscle
29	chr15:73524200-73546200	Weak transcription	Esophagus	oesophagus
30	chr15:73524200-73547000	Weak transcription	Ovary	ovary
31	chr15:73524400-73528400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr15:73524400-73531400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
33	chr15:73524400-73542200	Weak transcription	HUES48 Cell Line	embryonic stem cell
34	chr15:73524600-73530200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
35	chr15:73524800-73528800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr15:73524800-73538400	Weak transcription	H1 Cell Line	embryonic stem cell
37	chr15:73525000-73548800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr15:73525200-73528400	Weak transcription	Fetal Intestine Small	intestine
39	chr15:73525200-73528600	Weak transcription	Lung	lung
40	chr15:73525200-73530600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
41	chr15:73525200-73546200	Weak transcription	Fetal Muscle Leg	muscle
42	chr15:73525200-73547000	Weak transcription	Pancreas	Pancrea
43	chr15:73525400-73528600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
44	chr15:73525400-73530400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr15:73525400-73532000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr15:73525600-73528600	Weak transcription	Fetal Intestine Large	intestine
47	chr15:73525600-73547800	Weak transcription	Gastric	stomach
48	chr15:73526200-73528200	Enhancers	Brain Substantia Nigra	brain
49	chr15:73526200-73528600	Weak transcription	Fetal Stomach	stomach
50	chr15:73526400-73528000	Weak transcription	Rectal Mucosa Donor 31	rectum

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